df8c8dcd64bc7d71f9711df629b6d0178d6fa26f max Tue Feb 25 13:33:12 2020 -0800 trying to reduce the confusion in docs between refseq select and MANE, refs #24787 diff --git src/hg/makeDb/trackDb/refSeqComposite.html src/hg/makeDb/trackDb/refSeqComposite.html index 1e0002c..400e476 100644 --- src/hg/makeDb/trackDb/refSeqComposite.html +++ src/hg/makeDb/trackDb/refSeqComposite.html @@ -38,51 +38,53 @@ RefSeq Predicted – subset of RefSeq All that includes those annotations whose accessions begin with XM or XR.
  • RefSeq Other – all other annotations produced by the RefSeq group that do not fit the requirements for inclusion in the RefSeq Curated or the RefSeq Predicted tracks.
  • RefSeq Alignments – alignments of RefSeq RNAs to the $organism genome provided by the RefSeq group, following the display conventions for PSL tracks.
  • RefSeq Diffs – alignment differences between the $organism reference genome(s) and RefSeq transcripts. (Track not currently available for every assembly.)
  • - RefSeq HGMD – only show RefSeq Curated transcripts annotated by the Human - Gene Mutation Database. This track is only available on the human genomes hg19 and hg38. - It is the most restricted RefSeq subset, targeting clinical diagnostics. -
    • + UCSC RefSeq – annotations generated from UCSC's realignment of RNAs with NM + and NR accessions to the $organism genome. This track was previously known as the "RefSeq + Genes" track.
  • - RefSeq Select/MANE – only show transcript marked as RefSeq Select or MANE Select. + RefSeq Select+MANE (subset) – Subset of RefSeq Curated, transcripts marked as RefSeq Select or MANE Select. A single Select transcript is chosen as representative for each protein-coding gene. - Transcripts categorized as MANE are further agreed upon as representative by both NCBI + This track includes transcripts categorized as MANE, they are further agreed upon as representative by both NCBI RefSeq and Ensembl/GENCODE, and have a 100% identical match to a transcript in the Ensembl annotation. See NCBI RefSeq Select. + Note that we provide a separate track MANE, + which contains only the MANE transcripts, and not the ones specific to RefSeq.
  • - UCSC RefSeq – annotations generated from UCSC's realignment of RNAs with NM - and NR accessions to the $organism genome. This track was previously known as the "RefSeq - Genes" track.
    • + RefSeq HGMD (subset) – Subset of RefSeq Curated, transcripts annotated by the Human + Gene Mutation Database. This track is only available on the human genomes hg19 and hg38. + It is the most restricted RefSeq subset, targeting clinical diagnostics. +

    -The RefSeq All, RefSeq Curated, RefSeq Predicted, RefSeq Clinical, +The RefSeq All, RefSeq Curated, RefSeq Predicted, RefSeq HGMD, RefSeq Select/MANE and UCSC RefSeq tracks follow the display conventions for gene prediction tracks. The color shading indicates the level of review the RefSeq record has undergone: predicted (light), provisional (medium), or reviewed (dark), as defined by RefSeq.

    Color Level of review